The recent emergence of global ‘megafires’ has made it imperative to better understand the role of humans in altering the size, distribution, and seasonality of fires. The dynamic relationship between humans and fire is not a recent phenomenon; rather, fire has deep roots in our biological and cultural evolution. Because of its long-term perspective, archaeology is uniquely positioned to investigate the social and ecological drivers behind anthropogenic fire. However, the field faces challenges in creating solution-oriented research for managing fire in the future. In this dissertation, I originate new methods and approaches to archaeological data that enable us to interpret humans’ long-term influences on fire regimes. I weave together human niche construction theory and ecological resilience, creating connections between archaeology, paleoecology, and fire ecology. Three, stand-alone studies illustrate the usefulness of these methods and theories for charting changes in land-use, fire-regimes, and vegetation communities during the Neolithic Transition (7600 - 3800 cal. BP) in eastern Spain. In the first study (Ch. II), I analyze archaeological survey data using Bayesian methods to extract land-use intensities from mixed surface assemblages from a case study in the Canal de Navarrés. The second study (Ch. III) builds on the archaeological data collected computational model of landscape fire, charcoal dispersion, and deposition to test how multiple models of natural and anthropogenic fire activity contributed to the formation a single sedimentary charcoal dataset from the Canal de Navarrés. Finally, the third study (Ch. IV) incorporates the modeling and data generated in the previous chapters into sampling and analysis of sedimentary charcoal data from alluvial contexts in three study areas throughout eastern Spain. Results indicate that anthropogenic fire played a significant role in the creation of agricultural landscapes during the Neolithic period, but sustained, low-intensity burning after the late Neolithic period maintained the human created niche for millennia beyond the arrival of agro-pastoral land-use. With global fire activity on the rise, it is vital to incorporate perspectives on the origins, development, and maintenance of human-fire relationships to effectively manage fire in today’s coupled social-ecological landscapes.

Climate and environmental forcing are widely accepted to be important drivers of evolutionary and ecological change in mammal communities over geologic time scales. This paradigm has been particularly influential in studies of the eastern African late Cenozoic fossil record, in which aridification, increasing seasonality, and C4 grassland expansion are seen as having shaped the major patterns of human and faunal evolution. Despite the ubiquity of studies linking climate and environmental forcing to evolutionary and ecological shifts in the mammalian fossil record, many central components of this paradigm remain untested or poorly developed. To fill this gap, this dissertation employs biogeographical and macroecological analyses of present-day African mammal communities as a lens for understanding how abiotic change may have shaped community turnover and structure in the eastern African Plio-Pleistocene. Three dissertation papers address: 1) the role of ecological niche breadth in shaping divergent patterns of macroevolutionary turnover across clades; 2) the effect of climatic and environmental gradients on community assembly; 3) the relative influence of paleo- versus present-day climates in structuring contemporary patterns of community diversity. Results of these papers call into question many tenets of current theory, particularly: 1) that niche breadth differences (and, by extension, their influence on allopatric speciation) are important drivers of macroevolution, 2) that climate is more important than biotic interactions in community assembly, and 3) that communities today are in equilibrium with present-day climates. These findings highlight the need to critically reevaluate the role and scale-dependence of climate in mammal evolution and community ecology and to carefully consider potential time lags and disequilibrium dynamics in the fossil record.

This work investigates the effects of non-random sampling on our understanding of species distributions and their niches. In its most general form, bias is systematic error that can obscure interpretation of analytical results by skewing samples away from the average condition of the system they represent. Here I use species distribution modelling (SDM), virtual species, and multiscale geographically weighted regression (MGWR) to explore how sampling bias can alter our perception of broad patterns of biodiversity by distorting spatial predictions of habitat, a key characteristic in biogeographic studies. I use three separate case studies to explore: 1) How methods to account for sampling bias in species distribution modeling may alter estimates of species distributions and species-environment relationships, 2) How accounting for sampling bias in fossil data may change our understanding of paleo-distributions and interpretation of niche stability through time (i.e. niche conservation), and 3) How a novel use of MGWR can account for environmental sampling bias to reveal landscape patterns of local niche differences among proximal, but non-overlapping sister taxa. Broadly, my work shows that sampling bias present in commonly used federated global biodiversity observations is more than enough to degrade model performance of spatial predictions and niche characteristics. Measures commonly used to account for this bias can negate much loss, but only in certain conditions, and did not improve the ability to correctly identify explanatory variables or recreate species-environment relationships. Paleo-distributions calibrated on biased fossil records were improved with the use of a novel method to directly estimate the biased sampling distribution, which can be generalized to finer time slices for further paleontological studies. Finally, I show how a novel coupling of SDM and MGWR can illuminate local differences in niche separation that more closely match landscape genotypic variability in the two North American desert tortoise species than does their current taxonomic delineation.

Chytridiomycosis, an infectious disease caused by the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), has played a significant role in global amphibian declines. Researchers studying Bd aim to gain a better understanding of how this pathogen survives in unique microhabitats to promote persistence of amphibians in their natural habitat. The Arizona Game and Fish Department has worked for the last 12 years to recover populations of Chiricahua Leopard Frogs to ensure the species survives in the Huachuca Mountains in southeastern Arizona. During this time, the department tested for Bd throughout their release sites. As a result of large differences in prevalence noted in prior sampling for Bd in Miller and Ramsey canyons, I investigated abiotic factors that could explain these differences. I analyzed water samples from two canyons in the Huachuca Mountains and used nutrient analysis and filter extraction to test for differences in abiotic factors between these two sites that could affect Bd transmission. Results show that Ramsey Canyon was a positive site for Bd, while Miller Canyon remained negative. Results from water temperature estimates as well as a test for 30 elements revealed possible reasons for differences in Bd transmission between the two canyons.

Functional traits research has improved our understanding of how plants respond to their environments, identifying key trade-offs among traits. These studies primarily rely on correlative methods to infer trade-offs and often overlook traits that are difficult to measure (e.g., root traits, tissue senescence rates), limiting their predictive ability under novel conditions. I aimed to address these limitations and develop a better understanding of the trait space occupied by trees by integrating data and process models, spanning leaves to whole-trees, via modern statistical and computational methods. My first research chapter (Chapter 2) simultaneously fits a photosynthesis model to measurements of fluorescence and photosynthetic response curves, improving estimates of mesophyll conductance (gm) and other photosynthetic traits. I assessed how gm varies across environmental gradients and relates to other photosynthetic traits for 4 woody species in Arizona. I found that gm was lower at high aridity sites, varied little within a site, and is an important trait for obtaining accurate estimates of photosynthesis and related traits under dry conditions. Chapter 3 evaluates the importance of functional traits for whole-tree performance by fitting an individual-based model of tree growth and mortality to millions of measurements of tree heights and diameters to assess the theoretical trait space (TTS) of “healthy” North American trees. The TTS contained complicated, multi-variate structure indicative of potential trade-offs leading to successful growth. In Chapter 4, I applied an environmental filter (light stress) to the TTS, leading to simulated stand-level mortality rates up to 50%. Tree-level mortality was explained by 6 of the 32 traits explored, with the most important being radiation-use efficiency. The multidimentional space comprising these 6 traits differed in volume and location between trees that survived and died, indicating that selective mortality alters the TTS.

A species’ response to climate change depends on the interaction of biotic and abiotic factors that define future habitat suitability and species’ ability to migrate or adapt. The interactive effects of processes such as fire, dispersal, and predation have not been thoroughly addressed in the climate change literature. Our objective was to examine how life history traits, short-term global change perturbations, and long-term climate change interact to affect the likely persistence of an oak species - Quercus engelmannii (Engelmann oak). Specifically, we combined dynamic species distribution models, which predict suitable habitat, with stochastic, stage-based metapopulation models, which project population trajectories, to evaluate the effects of three global change factors – climate change, land use change, and altered fire frequency – emphasizing the roles of dispersal and seed predation. Our model predicted dramatic reduction in Q. engelmannii abundance, especially under drier climates and increased fire frequency. When masting lowers seed predation rates, decreased masting frequency leads to large abundance decreases. Current rates of dispersal are not likely to prevent these effects, although increased dispersal could mitigate population declines. The results suggest that habitat suitability predictions by themselves may under-estimate the impact of climate change for other species and locations.

Throughout the Southwest, complex geology and physiography concomitant with climatic variability contribute to diverse stream hydrogeomorphologies. Many riparian plant species store their seeds in soil seed banks, and germinate in response to moisture pulses, but the climatic controls of this response are poorly understood. To better understand the ecological implications of a changing climate on riparian plant communities, I investigated seed bank responses to seasonal temperature patterns and to stream hydrogeomorphic type. I asked the following questions: Are there distinct suites of warm and cool temperature germinating species associated with Southwestern streams; how do they differ between riparian and terrestrial zones, and between ephemeral and perennial streams? How does alpha diversity of the soil seed bank differ between streams with ephemeral, intermittent, and perennial flow, and between montane and basin streams? Do streams with greater elevational change have higher riparian zone seed bank beta-diversity? Does nestedness or turnover contribute more to within stream beta-diversity?

I collected soil samples from the riparian and terrestrial zones of 21 sites, placing them in growth chambers at one of two temperature regimes, and monitoring emergence of seedlings for 12 weeks. Results showed an approximately equal number of warm and cool specialists in both riparian and terrestrials zones; generalists also were abundant, particularly in the riparian zone. The number of temperature specialists and generalists in the riparian zones did not differ significantly between perennial headwater and ephemeral stream types. In montane streams, alpha diversity of the soil seed bank was highest for ephemeral reaches; in basin streams the intermittent and perennial reaches had higher diversity. Spatial turnover was primarily responsible for within stream beta-diversity—reaches had different species assemblages. The large portion of temperature specialists found in riparian seed banks indicates that even with available moisture riparian zone plant community composition will likely be impacted by changing temperatures. However, the presence of so many temperature generalists in the riparian zones suggests that some component of the seed bank is adapted to variable conditions and might offer resilience in a changing climate. Study results confirm the importance of conserving multiple hydrogeomorphic reach types because they support unique species assemblages.

Urban riparian corridors have the capacity to maintain high levels of abundance and biodiversity. Additionally, urban rivers also offer environmental amenities and can be catalysts for social and economic revitalization in human communities. Despite its importance for both humans and wildlife, blue space in cities used by waterbirds has received relatively little focus in urban bird studies. My principal objective was to determine how urbanization and water availability affect waterbird biodiversity in an arid city. I surveyed 36 transects stratified across a gradient of urbanization and water availability along the Salt River, a LTER long-term study system located in Phoenix, Arizona. Water physiognomy (shape and size) was the largest factor in shaping the bird community. Connectivity was an important element for waterbird diversity, but not abundance. Urbanization had guild-specific effects on abundance but was not important for waterbird diversity. Habitat-level environmental characteristics were more important than land use on waterbird abundance, as well as diversity. Diving and fish-eating birds were positively associated with large open bodies of water, whereas dabbling ducks, wading birds, and marsh species favored areas with large amounts of shoreline and emergent vegetation. My study supports that Phoenix blue space offers an important subsidy to migrating waterbird communities; while alternative habitat is not a replacement, it is important to consider as part of the larger conservation picture as traditional wetlands decline. Additionally, arid cities have the potential to support high levels of waterbird biodiversity, heterogeneous land use matrix can be advantageous in supporting regional diversity, and waterbirds are tolerant of urbanization if proper resources are provided via the habitat. The implications of this study are particularly relevant to urban planning in arid cities; Phoenix alone contains over 1,400 bodies of water, offering the opportunity to design and improve urban blue space to optimize potential habitat while providing public amenities.

Often, when thinking of cities we envision designed landscapes, where people regulate everything from water to weeds, ultimately resulting in an ecosystem decoupled from biophysical processes. It is unclear, however, what happens when the people regulating these extensively managed landscapes come under stress, whether from unexpected economic fluctuations or from changing climate norms. The overarching question of my dissertation research was: How does urban vegetation change in response to human behavior? To answer this question, I conducted multiscale research in an arid urban ecosystem as well as in a virtual desert city. I used a combination of long-term data and agent-based modeling to examine changes in vegetation across a range of measures influenced by biophysical, climate, institutional, and socioeconomic drivers. At the regional scale, total plant species diversity increased from 2000 to 2010, while species composition became increasingly homogeneous in urban and agricultural areas. At the residential scale, I investigated the effects of biophysical and socioeconomic drivers – the Great Recession of 2007-2010 in particular – on changing residential yard vegetation in Phoenix, AZ. Socioeconomic drivers affected plant composition and increasing richness, but the housing boom from 2000 through 2005 had a stronger influence on vegetation change than the subsequent recession. Surprisingly, annual plant species remained coupled to winter precipitation despite my expectation that their dynamics might be driven by socioeconomic fluctuations. In a modeling experiment, I examined the relative strength of psychological, social, and governance influences on large-scale urban land cover in a desert city. Model results suggested that social norms may be strong enough to lead to large-scale conversion to low water use residential landscaping, and governance may be unnecessary to catalyze residential landscape conversion under the pressure of extreme drought conditions. Overall, my dissertation research showed that urban vegetation is dynamic, even under the presumably stabilizing influence of human management activities. Increasing climate pressure, unexpected socioeconomic disturbances, growing urban populations, and shifting policies all contribute to urban vegetation dynamics. Incorporating these findings into planning policies will contribute to the sustainable management of urban ecosystems.